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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ), 'gf_id' => 'HOM05D001143', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001143' ), 'data_identifier' => 'HOM05D001143', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001143', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27410' => 'bna', 'A03p49100' => 'bna', 'Aa31LG2G15880' => 'aar', 'Aa31LG6G10310' => 'aar', 'Aa31LG7G13100' => 'aar', 'Aa31LG9G12700' => 'aar', 'Aa31LG9G2000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1278' => 'aag', 'Actinidia03602' => 'ach', 'Actinidia10813' => 'ach', 'Actinidia10814' => 'ach', 'Actinidia15286' => 'ach', 'Actinidia22580' => 'ach', 'Actinidia29848' => 'ach', 'Actinidia29849' => 'ach', 'Ah.01g008990' => 'amhyb', 'Ah.01g019800' => 'amhyb', 'Ah.01g019930' => 'amhyb', 'Ah.01g022690' => 'amhyb', 'Ah.09g232170' => 'amhyb', 'AL7G40110' => 'aly', 'AL8G18570' => 'aly', 'AL8G18730' => 'aly', 'Aqoxy1G03051' => 'aox', 'Aqoxy5G01749' => 'aox', 'Aqoxy5G01750' => 'aox', 'Aqoxy5G01751' => 'aox', 'Aqoxy5G01752' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B9A644' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DB4GMR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F73TU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H8DQQQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I2ECPT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQ1SRH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPFA7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5WKYJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VN8AVF' => 'arhy', 'AT4G15440' => 'ath', 'AT5G42650' => 'ath', 'ATR0681G188' => 'atr', 'ATR0681G341' => 'atr', 'ATR0733G240' => 'atr', 'Atru.chr13.579' => 'acertr', 'Atru.chr6.3227' => 'acertr', 'AUR62011392' => 'cqu', 'AUR62011393' => 'cqu', 'AUR62016665' => 'cqu', 'AUR62016666' => 'cqu', 'AUR62016667' => 'cqu', 'AUR62016668' => 'cqu', 'AUR62016669' => 'cqu', 'AUR62027399' => 'cqu', 'AUR62031312' => 'cqu', 'AUR62033870' => 'cqu', 'AUR62040103' => 'cqu', 'BcaB07g30608' => 'bca', 'BcaC03g16517' => 'bca', 'BcaC06g32934' => 'bca', 'BcaC06g33407' => 'bca', 'BolC2t10388H' => 'bol', 'BolC7t45235H' => 'bol', 'BraA02t07768Z' => 'bra', 'BraA03t14005Z' => 'bra', 'C02p43360' => 'bna', 'C07p47140' => 'bna', 'CAN.G1716.7' => 'can', 'CAN.G1716.8' => 'can', 'CAN.G290.8' => 'can', 'CAN.G309.21' => 'can', 'CAN.G322.91' => 'can', 'CAN.G322.92' => 'can', 'CAN.G322.93' => 'can', 'CAN.G371.110' => 'can', 'CAN.G371.111' => 'can', 'CANSAT25G0053' => 'cansat', 'CANSAT25G2789' => 'cansat', 'CANSAT56G1759' => 'cansat', 'CANSAT64G1222' => 'cansat', 'CANSAT78G1411' => 'cansat', 'CANSAT78G1761' => 'cansat', 'CANSAT78G2260' => 'cansat', 'CARHR181560' => 'chi', 'CARHR222200' => 'chi', 'Carub.0007s2648' => 'cru', 'Carub.0008s0638' => 'cru', 'Ca_01615_v3' => 'car', 'Ca_12483_v3' => 'car', 'Ca_15533_v3' => 'car', 'Ca_20825_v3' => 'car', 'Ca_30255_v3' => 'car', 'Cc00_g35930' => 'ccan', 'Cc02_g18120' => 'ccan', 'Cc02_g18130' => 'ccan', 'Cc05_g00930' => 'ccan', 'Cc05_g03650' => 'ccan', 'Cc10_g03570' => 'ccan', 'Cc10_g03580' => 'ccan', 'CDE01G0301' => 'cde', 'CDE02G2473' => 'cde', 'CDE04G0883' => 'cde', 'Cfa004957' => 'cfa', 'Cfa004958' => 'cfa', 'Cfa011261' => 'cfa', 'Cfa014340' => 'cfa', 'Cfa017762' => 'cfa', 'Cfa018464' => 'cfa', 'Ciclev10000825m.g' => 'ccl', 'Ciclev10014991m.g' => 'ccl', 'Ciclev10028333m.g' => 'ccl', 'CiPaw.04G113000' => 'cil', 'CiPaw.05G059300' => 'cil', 'CiPaw.15G068900' => 'cil', 'CiPaw.16G052300' => 'cil', 'ClCG00G003810' => 'cla', 'ClCG02G002090' => 'cla', 'ClCG02G005440' => 'cla', 'ClCG08G015460' => 'cla', 'COL.COLO4_17784' => 'col', 'COL.COLO4_21836' => 'col', 'COL.COLO4_26396' => 'col', 'Cpa.g.sc1880.1' => 'cpa', 'CsaV3_2G028330' => 'csa', 'CsaV3_7G003410' => 'csa', 'CsaV3_7G010160' => 'csa', 'CsaV3_7G010170' => 'csa', 'CSS0012232' => 'camsi', 'CSS0023501' => 'camsi', 'CSS0037941' => 'camsi', 'CSS0041775' => 'camsi', 'DCAR_012937' => 'dca', 'DCAR_019264' => 'dca', 'Dinv08746' => 'din', 'Dinv23572' => 'din', 'Dinv23573' => 'din', 'Dinv36023' => 'din', 'Dinv39366' => 'din', 'Dinv39730' => 'din', 'Duzib041G0214' => 'dzi', 'Duzib093G0269' => 'dzi', 'Duzib132G0846' => 'dzi', 'Duzib138G0376' => 'dzi', 'Duzib211G0414' => 'dzi', 'ECA234G1948' => 'eca', 'ECA236G1761' => 'eca', 'ECA247G1067' => 'eca', 'EL10Ac3g06219' => 'bvu', 'EL10Ac8g19325' => 'bvu', 'EL10Ac9g21784' => 'bvu', 'Eucgr.F01505' => 'egr', 'Eucgr.G00493' => 'egr', 'Eucgr.G00496' => 'egr', 'Eucgr.G00497' => 'egr', 'Eucgr.G00499' => 'egr', 'Eucgr.G00501' => 'egr', 'Eucgr.G00504' => 'egr', 'Eucgr.G00507' => 'egr', 'Eucgr.G01535' => 'egr', 'Eucgr.G01537' => 'egr', 'Eucgr.G01540' => 'egr', 'Eucgr.G01541' => 'egr', 'Eucgr.K00776' => 'egr', 'Eucgr.K01755' => 'egr', 'FAN02G4599' => 'fan', 'FAN05G3573' => 'fan', 'FAN09G1064' => 'fan', 'FAN11G0183' => 'fan', 'FAN14G1486' => 'fan', 'FAN15G2606' => 'fan', 'FAN15G2724' => 'fan', 'FAN15G3035' => 'fan', 'FAN15G3711' => 'fan', 'FAN18G0889' => 'fan', 'FAN20G0274' => 'fan', 'FAN20G1876' => 'fan', 'FAN20G2871' => 'fan', 'FAN20G2884' => 'fan', 'FAN24G1813' => 'fan', 'FAN24G2811' => 'fan', 'FAN24G3465' => 'fan', 'FAN27G2511' => 'fan', 'FvH4_2g07410' => 'fve', 'FvH4_2g07421' => 'fve', 'FvH4_2g07423' => 'fve', 'FvH4_2g40510' => 'fve', 'FvH4_3g17250' => 'fve', 'FvH4_5g16260' => 'fve', 'FvH4_6g42740' => 'fve', 'Glyma.04G035000' => 'gma', 'Glyma.07G162900' => 'gma', 'Glyma.11G122700' => 'gma', 'Glyma.12G047600' => 'gma', 'Glyma.12G191400' => 'gma', 'Glyma.14G078600' => 'gma', 'Glyma.17G246500' => 'gma', 'Gohir.A03G115300' => 'ghi', 'Gohir.A04G115850' => 'ghi', 'Gohir.A04G115900' => 'ghi', 'Gohir.A05G260700' => 'ghi', 'Gohir.A06G013200' => 'ghi', 'Gohir.A06G013400' => 'ghi', 'Gohir.A11G154300' => 'ghi', 'Gohir.A12G030400' => 'ghi', 'Gohir.A12G030500' => 'ghi', 'Gohir.D02G093300' => 'ghi', 'Gohir.D05G262900' => 'ghi', 'Gohir.D06G010700' => 'ghi', 'Gohir.D06G010800' => 'ghi', 'Gohir.D06G010901' => 'ghi', 'Gohir.D06G011000' => 'ghi', 'Gohir.D11G161100' => 'ghi', 'Gohir.D12G041900' => 'ghi', 'Gohir.D12G042100' => 'ghi', 'Gorai.005G105800' => 'gra', 'Gorai.007G171600' => 'gra', 'Gorai.008G043900' => 'gra', 'Gorai.008G044100' => 'gra', 'Gorai.009G274700' => 'gra', 'Gorai.010G013600' => 'gra', 'Gorai.010G013700' => 'gra', 'GSVIVG01009616001' => 'vvi', 'GSVIVG01030474001' => 'vvi', 'GSVIVG01031885001' => 'vvi', 'GSVIVG01031887001' => 'vvi', 'GSVIVG01031888001' => 'vvi', 'HanXRQChr04g0104381' => 'han', 'HanXRQChr04g0126981' => 'han', 'HanXRQChr09g0268351' => 'han', 'HanXRQChr09g0268361' => 'han', 'HanXRQChr10g0307551' => 'han', 'HanXRQChr16g0506541' => 'han', 'Haze_02450' => 'cav', 'Haze_02519' => 'cav', 'Haze_02521' => 'cav', 'Haze_12801' => 'cav', 'Haze_17602' => 'cav', 'Haze_17604' => 'cav', 'Hma1.2p1_0260F.1_g104430' => 'hma', 'Hma1.2p1_0842F.1_g227090' => 'hma', 'Hma1.2p1_0842F.1_g227100' => 'hma', 'Hma1.2p1_1630F.1_g294570' => 'hma', 'HPP92_008824' => 'vpl', 'HPP92_019642' => 'vpl', 'HPP92_023070' => 'vpl', 'Hund10224' => 'sun', 'Lalb_Chr03g0025931' => 'lal', 'Lalb_Chr08g0245751' => 'lal', 'Lalb_Chr10g0095371' => 'lal', 'Lalb_Chr14g0368961' => 'lal', 'Lalb_Chr14g0375871' => 'lal', 'Lalb_Chr17g0338241' => 'lal', 'Lalb_Chr17g0338251' => 'lal', 'Lalb_Chr23g0266751' => 'lal', 'Lj1C778T5' => 'lonja', 'Lj1C778T6' => 'lonja', 'Lj1g0006570' => 'lja', 'Lj1P773T27' => 'lonja', 'Lj2g0019752' => 'lja', 'Lj2g0023324' => 'lja', 'Lj3g0027475' => 'lja', 'Lj4A782T77' => 'lonja', 'Lj4C47T10' => 'lonja', 'Lj4P781T76' => 'lonja', 'Lj5g0027886' => 'lja', 'Lj5P203T43' => 'lonja', 'Lj8A127T47' => 'lonja', 'LjContig00274_ERROPOS1100000g0011669' => 'lja', 'Lsat_1_v5_gn_1_19560' => 'lsa', 'Lsat_1_v5_gn_2_86441' => 'lsa', 'Lsat_1_v5_gn_3_26481' => 'lsa', 'Lsat_1_v5_gn_3_4080' => 'lsa', 'Lsat_1_v5_gn_4_122621' => 'lsa', 'Lsat_1_v5_gn_4_122741' => 'lsa', 'Lsat_1_v5_gn_4_35481' => 'lsa', 'Lsat_1_v5_gn_5_117261' => 'lsa', 'Lsat_1_v5_gn_5_117301' => 'lsa', 'Lsat_1_v5_gn_6_79200' => 'lsa', 'Lsat_1_v5_gn_7_88460' => 'lsa', 'Lsat_1_v5_gn_7_93220' => 'lsa', 'Manes.05G166200' => 'mes', 'Manes.05G166301' => 'mes', 'Manes.12G072001' => 'mes', 'Manes.15G146200' => 'mes', 'Manes.18G031800' => 'mes', 'Manes.18G031933' => 'mes', 'Mapoly0160s0030' => 'mpo', 'Mapoly0185s0014' => 'mpo', 'MBI05_g36571_MAGBIO' => 'mbi', 'MBI07_g01732_MAGBIO' => 'mbi', 'MBI07_g01733_MAGBIO' => 'mbi', 'MBI16_g11011_MAGBIO' => 'mbi', 'MBI16_g17457_MAGBIO' => 'mbi', 'MBI16_g29184_MAGBIO' => 'mbi', 'MBI16_g31338_MAGBIO' => 'mbi', 'MBI16_g46206_MAGBIO' => 'mbi', 'MD00G1038400' => 'mdo', 'MD08G1038600' => 'mdo', 'MD09G1071400' => 'mdo', 'MD10G1085800' => 'mdo', 'MD17G1100800' => 'mdo', 'Medtr1g021652' => 'mtr', 'Medtr1g034320' => 'mtr', 'Medtr1g034330' => 'mtr', 'Medtr2g087890' => 'mtr', 'Medtr3g111530' => 'mtr', 'Medtr4g068550' => 'mtr', 'MELO3C010910.2' => 'cme', 'MELO3C018412.2' => 'cme', 'MELO3C018413.2' => 'cme', 'MELO3C018833.2' => 'cme', 'Migut.B00287' => 'egut', 'Migut.C00664' => 'egut', 'Migut.M00433' => 'egut', 'Migut.M00434' => 'egut', 'Migut.N01221' => 'egut', 'Migut.N02681' => 'egut', 'Migut.O00603' => 'egut', 'MSTRG.16783' => 'ama', 'MSTRG.22281' => 'ama', 'MSTRG.24313' => 'ama', 'MSTRG.25130' => 'ama', 'MSTRG.27712' => 'ama', 'MSTRG.6581' => 'ama', 'Nitab4.5_0000110g0020' => 'nta', 'Nitab4.5_0000130g0230' => 'nta', 'Nitab4.5_0000215g0040' => 'nta', 'Nitab4.5_0002525g0030' => 'nta', 'Nitab4.5_0003168g0010' => 'nta', 'Nitab4.5_0003281g0080' => 'nta', 'Nitab4.5_0003727g0010' => 'nta', 'Nitab4.5_0003727g0020' => 'nta', 'Nitab4.5_0004126g0030' => 'nta', 'Nitab4.5_0004479g0070' => 'nta', 'Nitab4.5_0006248g0010' => 'nta', 'Nitab4.5_0008189g0010' => 'nta', 'Nitab4.5_0008239g0010' => 'nta', 'Nitab4.5_0008507g0010' => 'nta', 'Nitab4.5_0008753g0020' => 'nta', 'Nitab4.5_0012894g0010' => 'nta', 'Nitab4.5_0015407g0010' => 'nta', 'Nitab4.5_0017161g0010' => 'nta', 'Nn1g00066' => 'nnu', 'Nn5g29425' => 'nnu', 'Nn5g29427' => 'nnu', 'Nn5g29428' => 'nnu', 'Nn6g32159' => 'nnu', 'Oeu003711.1' => 'oeu', 'Oeu004681.1' => 'oeu', 'Oeu009587.1' => 'oeu', 'Oeu015612.1' => 'oeu', 'Oeu019005.1' => 'oeu', 'Oeu027598.1' => 'oeu', 'Os02g0110200' => 'osa', 'Os02g0218700' => 'osa', 'Os02g0218800' => 'osa', 'Os03g0225900' => 'osa', 'Os03g0767000' => 'osa', 'Peaxi162Scf00007g00122' => 'pax', 'Peaxi162Scf00016g01146' => 'pax', 'Peaxi162Scf00016g01221' => 'pax', 'Peaxi162Scf00016g01228' => 'pax', 'Peaxi162Scf00115g00115' => 'pax', 'Peaxi162Scf00280g00065' => 'pax', 'Peaxi162Scf00684g00511' => 'pax', 'Peaxi162Scf00684g00578' => 'pax', 'PGR083G1502' => 'pgr', 'PGR102G1881' => 'pgr', 'PGR142G0750' => 'pgr', 'PGSC0003DMG400001078' => 'stu', 'PGSC0003DMG400001149' => 'stu', 'PGSC0003DMG400010557' => 'stu', 'PGSC0003DMG400016887' => 'stu', 'PGSC0003DMG400025158' => 'stu', 'PGSC0003DMG400025159' => 'stu', 'Phvul.001G017800' => 'pvu', 'Phvul.003G010700' => 'pvu', 'Phvul.005G116800' => 'pvu', 'Phvul.007G055700' => 'pvu', 'Phvul.009G061325' => 'pvu', 'Phvul.011G049600' => 'pvu', 'Potri.002G130700' => 'ptr', 'Potri.004G148600' => 'ptr', 'Potri.004G148900' => 'ptr', 'Potri.004G149000' => 'ptr', 'Potri.009G109700' => 'ptr', 'Potri.014G038700' => 'ptr', 'Potri.014G155800' => 'ptr', 'Pp3c1_7150' => 'ppa', 'Pp3c5_3300' => 'ppa', 'Pp3c7_25640' => 'ppa', 'Prupe.1G386300' => 'ppe', 'Prupe.3G213800' => 'ppe', 'Prupe.7G014000' => 'ppe', 'Prupe.8G110100' => 'ppe', 'Psat0s2724g0160' => 'psa', 'Psat0s3268g0280' => 'psa', 'Psat1g093440' => 'psa', 'Psat5g263320' => 'psa', 'Psat6g011000' => 'psa', 'Psat6g097160' => 'psa', 'Psat7g207240' => 'psa', 'PSO170G2081' => 'pso', 'PSO170G2916' => 'pso', 'PSO210G1166' => 'pso', 'PSO210G4521' => 'pso', 'PSO210G5865' => 'pso', 'PSO210G7139' => 'pso', 'PSO210G7757' => 'pso', 'PSO210G7792' => 'pso', 'PSO541G0480' => 'pso', 'PSO541G1925' => 'pso', 'PSO675G0352' => 'pso', 'PSO675G5759' => 'pso', 'PSO675G6064' => 'pso', 'PSO700G0132' => 'pso', 'QL02p007013' => 'qlo', 'QL05p013860' => 'qlo', 'QL08p031573' => 'qlo', 'QL08p031583' => 'qlo', 'QL11p039432' => 'qlo', 'QL11p039446' => 'qlo', 'QL11p039470' => 'qlo', 'QL11p039493' => 'qlo', 'QL11p039515' => 'qlo', 'QL11p039533' => 'qlo', 'QL12p006794' => 'qlo', 'RcHm_v2.0_Chr2g0158631' => 'rch', 'RcHm_v2.0_Chr6g0260901' => 'rch', 'RcHm_v2.0_Chr6g0260921' => 'rch', 'RcHm_v2.0_Chr6g0260931' => 'rch', 'RcHm_v2.0_Chr6g0260961' => 'rch', 'RcHm_v2.0_Chr6g0261011' => 'rch', 'RcHm_v2.0_Chr6g0300221' => 'rch', 'Rhsim04G0052300' => 'rsi', 'Rhsim06G0039400' => 'rsi', 'Rhsim07G0234400' => 'rsi', 'Rhsim11G0171200' => 'rsi', 'Rhsim11G0171300' => 'rsi', 'Sabra02G0102800' => 'sbr', 'Sabra04G0098700' => 'sbr', 'Sabra04G0098900' => 'sbr', 'Sabra09G0083800' => 'sbr', 'Sabra14G0028100' => 'sbr', 'Sabra14G0117800' => 'sbr', 'SalBow6G4792' => 'sbo', 'SalBow6G6848' => 'sbo', 'SalBow7G3041' => 'sbo', 'SalBow7G3133' => 'sbo', 'SalBow8G3724' => 'sbo', 'Sc06g0009600' => 'sci', 'Sc15g0006670' => 'sci', 'Sc18g0004760' => 'sci', 'Sed0000461' => 'sed', 'Sed0006920' => 'sed', 'Sed0018122' => 'sed', 'Sed0018917' => 'sed', 'Sed0019712' => 'sed', 'SEGI_00283' => 'sgi', 'SEGI_05408' => 'sgi', 'SEGI_06161' => 'sgi', 'SEGI_22254' => 'sgi', 'SEGI_26627' => 'sgi', 'SEGI_37367' => 'sgi', 'SEGI_40017' => 'sgi', 'SEGI_40380' => 'sgi', 'SGA_v2.0_scaffold33G13549' => 'sas', 'SGA_v2.0_scaffold34G13756' => 'sas', 'SGA_v2.0_scaffold58G20590' => 'sas', 'SHI08190' => 'shi', 'SMO116G0191' => 'smo', 'SMO147G0067' => 'smo', 'SMO147G0094' => 'smo', 'SMO147G0384' => 'smo', 'SMO165G0028' => 'smo', 'SMO165G0078' => 'smo', 'SMO165G0081' => 'smo', 'SMO203G0275' => 'smo', 'SMO252G0004' => 'smo', 'SMO272G0031' => 'smo', 'SMO356G0385' => 'smo', 'Solyc01g109140.3' => 'sly', 'Solyc01g109150.4' => 'sly', 'Solyc01g109160.4' => 'sly', 'Solyc04g079730.1' => 'sly', 'Solyc07g049690.3' => 'sly', 'Solyc10g007960.1' => 'sly', 'Solyc11g069800.1' => 'sly', 'Sopen01g051340' => 'spe', 'Sopen01g051350' => 'spe', 'Sopen01g051360' => 'spe', 'Sopen04g033310' => 'spe', 'Sopen07g025110' => 'spe', 'Sopen07g025290' => 'spe', 'Sopen10g003830' => 'spe', 'Sopen11g028480' => 'spe', 'Sp2g07070' => 'spa', 'Sp7g13660' => 'spa', 'TAR624G1244' => 'tar', 'TAR625G0489' => 'tar', 'TAR628G1354' => 'tar', 'THA.LOC104803399' => 'tha', 'THA.LOC104806952' => 'tha', 'THA.LOC104819457' => 'tha', 'THA.LOC104820221' => 'tha', 'Thecc.01G177900' => 'tca', 'Thecc.02G029500' => 'tca', 'Thecc.08G019700' => 'tca', 'Thhalv10003180m.g' => 'esa', 'Thhalv10025050m.g' => 'esa', 'TPR.G10221' => 'tpr', 'TPR.G10236' => 'tpr', 'TPR.G12391' => 'tpr', 'TPR.G15749' => 'tpr', 'TPR.G18599' => 'tpr', 'TPR.G18604' => 'tpr', 'TPR.G4240' => 'tpr', 'TWI12G0614' => 'twi', 'TWI12G0789' => 'twi', 'TWI36G0969' => 'twi', 'TWI36G1060' => 'twi', 'unitig_21.g20765' => 'ugi', 'unitig_22.g6776' => 'ugi', 'vmacro02156' => 'vma', 'vmacro04482' => 'vma', 'vmacro04483' => 'vma', 'vmacro09344' => 'vma', 'vmacro21594' => 'vma', 'VMungo0464G0671' => 'vmu', 'VMungo0464G1674' => 'vmu', 'VMungo0647G0511' => 'vmu', 'VMungo0647G1397' => 'vmu', 'VMungo0647G1661' => 'vmu', 'VMungo0720G2792' => 'vmu', 'VMungo1080G1732' => 'vmu', 'VMungo1127G1363' => 'vmu', 'VMungo1215G1317' => 'vmu', 'VMungo1309G2555' => 'vmu', 'Zm00001eb009340' => 'zma', 'Zm00001eb058640' => 'zma', 'Zm00001eb058670' => 'zma', 'Zm00001eb205210' => 'zma', 'Zm00001eb209760' => 'zma', 'Zm00001eb214000' => 'zma' ) $gf_id = 'HOM05D001143' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001143' ) $data_identifier = 'HOM05D001143' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 11, 'bca' => (int) 4, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 9, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 5, 'ccan' => (int) 7, 'cde' => (int) 3, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 2, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 18, 'fve' => (int) 7, 'gma' => (int) 7, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 12, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 6, 'nta' => (int) 18, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 14, 'qlo' => (int) 11, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 11, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 10, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb214000' $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